Rainfall data is the most basic input data to analyze the hydrological phenomena and can be missing due to various reasons. In this research, a neural network based model to estimate missing rainfall data as approximate values was developed for 12 rainfall stations in the Soyang river basin to improve existing methods. This approach using neural network has shown to be useful in many applications to deal with complicated natural phenomena and displayed better results compared to the popular offline estimating methods, such as RDS(Reciprocal Distance Squared) method and AMM(Arithmetic Mean Method). Additionally, we proposed automated data reconciliation systems composed of a neural network learning processer to be capable of real-time reconciliation to transmit reliable hydrological data online.